Retrieves a complete, stochastically-resolved phylogeny via the Fish Tree of Life API. If neither `species` nor `rank` are specified, returns the entire phylogeny.

fishtree_complete_phylogeny(species, rank,
  mc.cores = getOption("mc.cores", 1L))



(Optionally) subset the results based on a vector of species names.


(Optionally) subset the results based on the supplied taxonomic rank.


Number of cores to use in mclapply when subsetting the tree (default `1`)


An object of class `"multiPhylo"`.


Rabosky, D. L., Chang, J., Title, P. O., Cowman, P. F., Sallan, L., Friedman, M., Kashner, K., Garilao, C., Near, T. J., Coll, M., Alfaro, M. E. (2018). An inverse latitudinal gradient in speciation rate for marine fishes. Nature, 559(7714), 392–395. doi:10.1038/s41586-018-0273-1

Enhanced polytomy resolution strengthens evidence for global gradient in speciation rate for marine fishes.


if (FALSE) { tree <- fishtree_complete_phylogeny(rank = "Acanthuridae") sampled_tips <- fishtree_phylogeny(rank = "Acanthuridae")$tip.label all_tips <- tree[[1]]$tip.label new_tips <- setdiff(all_tips, sampled_tips) par(mfrow = c(2,2)) for (ii in 1:4) { plot(tree[[ii]], show.tip.label = FALSE, no.margin = TRUE) ape::tiplabels(pch = 19, col = ifelse(tree[[ii]]$tip.label %in% new_tips, "red", NA)) } }